Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

2YXT

Human Pyridoxal Kinase

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0000287	molecular_function	magnesium ion binding
A	0005524	molecular_function	ATP binding
A	0005576	cellular_component	extracellular region
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005829	cellular_component	cytosol
A	0008270	molecular_function	zinc ion binding
A	0008478	molecular_function	pyridoxal kinase activity
A	0009443	biological_process	pyridoxal 5'-phosphate salvage
A	0016301	molecular_function	kinase activity
A	0016740	molecular_function	transferase activity
A	0016773	molecular_function	phosphotransferase activity, alcohol group as acceptor
A	0030170	molecular_function	pyridoxal phosphate binding
A	0030955	molecular_function	potassium ion binding
A	0031402	molecular_function	sodium ion binding
A	0031403	molecular_function	lithium ion binding
A	0034774	cellular_component	secretory granule lumen
A	0035580	cellular_component	specific granule lumen
A	0042803	molecular_function	protein homodimerization activity
A	0042817	biological_process	pyridoxal metabolic process
A	0042818	biological_process	pyridoxamine metabolic process
A	0042822	biological_process	pyridoxal phosphate metabolic process
A	0046872	molecular_function	metal ion binding
A	0070062	cellular_component	extracellular exosome
B	0000166	molecular_function	nucleotide binding
B	0000287	molecular_function	magnesium ion binding
B	0005524	molecular_function	ATP binding
B	0005576	cellular_component	extracellular region
B	0005634	cellular_component	nucleus
B	0005654	cellular_component	nucleoplasm
B	0005829	cellular_component	cytosol
B	0008270	molecular_function	zinc ion binding
B	0008478	molecular_function	pyridoxal kinase activity
B	0009443	biological_process	pyridoxal 5'-phosphate salvage
B	0016301	molecular_function	kinase activity
B	0016740	molecular_function	transferase activity
B	0016773	molecular_function	phosphotransferase activity, alcohol group as acceptor
B	0030170	molecular_function	pyridoxal phosphate binding
B	0030955	molecular_function	potassium ion binding
B	0031402	molecular_function	sodium ion binding
B	0031403	molecular_function	lithium ion binding
B	0034774	cellular_component	secretory granule lumen
B	0035580	cellular_component	specific granule lumen
B	0042803	molecular_function	protein homodimerization activity
B	0042817	biological_process	pyridoxal metabolic process
B	0042818	biological_process	pyridoxamine metabolic process
B	0042822	biological_process	pyridoxal phosphate metabolic process
B	0046872	molecular_function	metal ion binding
B	0070062	cellular_component	extracellular exosome

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE NA A 1314

Chain	Residue
A	ASP113
A	HOH1320
A	HOH1321
A	HOH1322
A	HOH1323
A	HOH1324

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA B 1316

Chain	Residue
B	HOH1352
B	HOH1353
B	THR186
B	HOH1350
B	HOH1351

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE PO4 A 1319

Chain	Residue
A	GLN63
A	ARG70
A	MET93
A	GLU100
A	HOH1451

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE PO4 B 1329

Chain	Residue
B	GLY32
B	HIS246
B	LYS247
B	HOH1582

site_id	AC5
Number of Residues	2
Details	BINDING SITE FOR RESIDUE PO4 B 1335

Chain	Residue
B	ILE223
B	ARG224

site_id	AC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE PO4 B 1337

Chain	Residue
B	GLY179
B	ASP181
B	HOH1384
B	HOH1385

site_id	AC7
Number of Residues	2
Details	BINDING SITE FOR RESIDUE PO4 B 1347

Chain	Residue
B	GLU155
B	LYS161

site_id	AC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE PO4 B 1349

Chain	Residue
B	GLN63
B	TYR66
B	ARG70
B	ASP96
B	GLU100

site_id	AC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MPD A 1001

Chain	Residue
A	SER12
A	THR47
A	HOH1365
A	HOH1441
A	HOH1478

site_id	BC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MPD A 1003

Chain	Residue
A	THR186
A	GLY234
A	LEU263

site_id	BC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MPD A 1005

Chain	Residue
A	ARG224
A	HIS264
A	GLN268

site_id	BC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MPD A 1009

Chain	Residue
A	GLY32
A	HIS246
A	LYS247
A	HOH1536

site_id	BC4
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MPD A 1013

Chain	Residue
A	ILE223
A	ARG224

site_id	BC5
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MPD B 1023

Chain	Residue
B	THR186
B	HOH1497

site_id	BC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MPD B 1025

Chain	Residue
B	ILE223
B	ARG224
B	HIS264
B	GLN268

site_id	BC7
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MPD B 1027

Chain	Residue
B	ASP181

site_id	BC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MPD B 1031

Chain	Residue
B	SER12
B	HIS46
B	THR47
B	HOH1455

site_id	BC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MPD B 1033

Chain	Residue
B	PHE43
B	TYR84
B	ARG86

site_id	CC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MPD B 1039

Chain	Residue
B	GLU130
B	LEU156
B	HOH1496
B	HOH1502

site_id	CC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MPD B 1041

Chain	Residue
B	SER177
B	ARG206
B	LEU312

site_id	CC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MPD B 1045

Chain	Residue
B	THR47
B	TYR84
B	TYR127

site_id	CC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE MPD B 1053

Chain	Residue
B	GLN205
B	THR245
B	PRO249
B	HOH1392
B	HOH1428
B	HOH1437
B	HOH1574

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	2
Details	Active site: {"description":"Proton acceptor","evidences":[{"source":"PubMed","id":"19351586","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"PubMed","id":"19351586","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3FHX","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"OCT-2009","submissionDatabase":"PDB data bank","title":"Crystal structure of PL kinase in complex with MgATP and PLP: Structural basis of severe induced MgATP substrate inhibition of the enzyme.","authors":["Gandhi A.K.","Musayev F.N.","Safo M.K."]}},{"source":"PDB","id":"3KEU","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"PubMed","id":"19351586","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22879864","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3FHX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4EN4","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"PubMed","id":"17766369","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19351586","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22879864","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"OCT-2009","submissionDatabase":"PDB data bank","title":"Crystal structure of PL kinase in complex with MgATP and PLP: Structural basis of severe induced MgATP substrate inhibition of the enzyme.","authors":["Gandhi A.K.","Musayev F.N.","Safo M.K."]}},{"source":"PDB","id":"3FHX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3KEU","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4EN4","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"17766369","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19351586","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22879864","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"OCT-2009","submissionDatabase":"PDB data bank","title":"Crystal structure of PL kinase in complex with MgATP and PLP: Structural basis of severe induced MgATP substrate inhibition of the enzyme.","authors":["Gandhi A.K.","Musayev F.N.","Safo M.K."]}},{"source":"PDB","id":"2YXT","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3FHX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3KEU","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4EN4","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"PubMed","id":"19351586","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"OCT-2009","submissionDatabase":"PDB data bank","title":"Crystal structure of PL kinase in complex with MgATP and PLP: Structural basis of severe induced MgATP substrate inhibition of the enzyme.","authors":["Gandhi A.K.","Musayev F.N.","Safo M.K."]}},{"source":"PDB","id":"3FHY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3KEU","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"17766369","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19351586","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22879864","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"OCT-2009","submissionDatabase":"PDB data bank","title":"Crystal structure of PL kinase in complex with MgATP and PLP: Structural basis of severe induced MgATP substrate inhibition of the enzyme.","authors":["Gandhi A.K.","Musayev F.N.","Safo M.K."]}},{"source":"PDB","id":"2YXU","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3FHX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3FHY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3KEU","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4EN4","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"22879864","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"OCT-2009","submissionDatabase":"PDB data bank","title":"Crystal structure of PL kinase in complex with MgATP and PLP: Structural basis of severe induced MgATP substrate inhibition of the enzyme.","authors":["Gandhi A.K.","Musayev F.N.","Safo M.K."]}},{"source":"PDB","id":"3KEU","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4EN4","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"PubMed","id":"19351586","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"OCT-2009","submissionDatabase":"PDB data bank","title":"Crystal structure of PL kinase in complex with MgATP and PLP: Structural basis of severe induced MgATP substrate inhibition of the enzyme.","authors":["Gandhi A.K.","Musayev F.N.","Safo M.K."]}},{"source":"PDB","id":"3FHX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3KEU","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	4
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"19369195","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18691976","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"19369195","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI13
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18691976","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"19369195","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

Catalytic Information from CSA

site_id	CSA1
Number of Residues	4
Details	Annotated By Reference To The Literature 1tz3

Chain	Residue	Details
A	GLY234
A	THR233
A	GLY232
A	ASP235

site_id	CSA2
Number of Residues	4
Details	Annotated By Reference To The Literature 1tz3

Chain	Residue	Details
B	GLY234
B	THR233
B	GLY232
B	ASP235

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)